# CI

0th

Percentile

##### Consistency Index and Retention Index

CI and RI compute the Consistency Index (CI) and Retention Index (RI).

##### Usage
CI(tree, data, cost = NULL, sitewise = FALSE)RI(tree, data, cost = NULL, sitewise = FALSE)
##### Arguments
tree

tree to start the nni search from.

data

A object of class phyDat containing sequences.

cost

A cost matrix for the transitions between two states.

sitewise

return CI/RI for alignment or sitewise

##### Details

The Consistency Index is defined as minimum number of changes divided by the number of changes required on the tree (parsimony score). The Consistency Index is equal to one if there is no homoplasy. And the Retention Index is defined as $$RI = \frac{MaxChanges - ObsChanges}{MaxChanges - MinChanges}$$

parsimony, pratchet, fitch, sankoff, bab, ancestral.pars